Janeway has a miserable headache. The pain affects her normal scientific curiosity; Chakotay's enthusiasm over some binary pulsars goes unshared. And neither of them notices that something is aboard the ship, carefully scanning each member of the crew.

When Chakotay begins aging rapidly, the Doctor's scan detects that segments of his DNA have been hyperstimulated. Neelix has a different ailment, but the Doctor finds segments of his DNA are also hyperstimulated. Soon, others are coming in with obscure genetic problems. Torres and the Doctor find microscopic tags on the crewmembers' DNA, but before they can investigate further, the Doctor's program is deactivated and Torres collapses.

Later, the Doctor taps into Seven of Nine's audio implants to ask her to meet him in the holodeck. He adjusts her Borg sensory nodes so she can scan Voyager for anything unusual. Suddenly, Seven can see aliens everywhere, invisibly prodding crewmembers with instruments. She goes to the Captain and finds Janeway flanked by aliens sticking needles into her head — the source of her headaches.

Seven tells the Doctor that the aliens are performing medical experiments on the crew. She could make them visible with a modulated phaser beam, but the Doctor believes they might retaliate. He suggests that delivering a simultaneous neuroleptic shock to each member of the crew will undo the experiments. But when Seven tries to implement the plan, Tuvok stops her, misunderstanding her intentions. The aliens realize she can see them, and Seven is forced to use her phaser to make one visible. She brings it to Janeway, who is outraged when the alien — a Srivani — explains they are using the data to cure disorders within their race. The Srivani threatens to kill everyone if the experiments are not allowed to continue.

The Captain feels it's time for desperate measures. She steers Voyager into the binary pulsar, knowing it means almost certain destruction. The Srivani evacuate the ship as Voyager plunges through at full throttle. The ship comes out relatively unscathed and the Doctor is able to neutralize the effects of the experiments, allowing them to continue the tedious voyage toward home.